City University New York, Brooklyn College receives an award to develop a tandem repeat database. Tandemly repeated DNA sequences are widespread throughout the human genome. They show suffcient variability among individuals in a population that they have become important in several fields. Researchers have been using tandem repeats in many areas including human identity testing (DNA fingerprinting), mapping studies, population studies, and gene prediction. This project creates a database containing an accounting of all tandem repeats within the human genome with bounded copy-to-copy differences. The steps include Design of an algorithm that finds all tandem repeats within a sequence; Implementing the algorithm in C++ or Java; Design of a website, and uploading the program as open-source code. The software will be run on the sequences of the human genome and stored in a database of results. At the end the results will be evaluated by comparing them to the repeats found using heuristic approaches. The proposed algorithm will be implemented by undergraduate students, satisfying the requirement each student has of completing a research project with a faculty member. Furthermore, the algorithm will be incorporated into a new undergraduate course on Computational Biology. Research results will be disseminated through major conferences and journal publications. A website will be created to enable others access to the source code and database.
